Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37059.89 
• Atom Count: 2606 
• Residue Count: 340 
• Unique protein chains: 2

1RMH

RECOMBINANT CYCLOPHILIN A FROM HUMAN T CELL

• DOI: 10.2210/pdb1RMH/pdb

• Classification: ISOMERASE/ ISOMERASE SUBSTRATE
• Organism(s): Homo sapiens


• Deposited: 1995-07-31 Released: 1996-10-14 
• Deposition Author(s): Zhao, Y., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Work: 0.189 

Literature

Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization.

Zhao, Y., Ke, H.

(1996) Biochemistry 35: 7356-7361

• PubMed: 8652511 
• DOI: 10.1021/bi9602775


• PubMed Abstract: 
  

The crystal structure of human recombinant cyclophilin A complexed with a substrate of succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (AAPF) has been determined and refined to an R-factor of 0.189 at 2.4 A resolution. The structure revealed only the cis form of the substrate bound to cyclophilin A in a stoichiometry of 1:1. This binding ratio is different from the structure of cyclophilin A complexed with the tetrapeptide N-acetyl-Ala-Ala-Pro-Ala-amidomethylcourmarin. Model docking revealed that the trans form of AAPF does not fit into the active site. The observation that only the trans cis form of AAPF binds to cyclophilin A implies that cyclophilin A predominantly catalyzes the trans to cis isomerization of a peptidylprolyl amide bond. On the basis of the structure, it is proposed that Arg55 hydrogen-bonds to the nitrogen to deconjugate the resonance of the prolyl amide bond and thus facilitates the cis-trans rotation.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYCLOPHILIN A	A, B	164	Homo sapiens	Mutation(s): 0  Gene Names: PPIA (CYPA) EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Go to Gene View: PPIA Go to UniProtKB:  P62937

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
AAPF PEPTIDE SUBSTRATE	C, D	6	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SIN	C, D	NON-POLYMER	C4 H6 O4		--
NIT	C, D	NON-POLYMER	C6 H6 N2 O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Work: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 37.800	α = 90.00
b = 109.200	β = 90.00
c = 118.700	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-07-31 
• Released Date: 1996-10-14 
• Deposition Author(s): Zhao, Y., Ke, H.

Revision History 

• Version 1.0: 1996-10-14
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-11-29
  Type: Derived calculations, Other